Population genomic data contains a startling amount of information about the demographic history of populations. As advances in statistical methodology for demographic inference and increases in sampling provide greater resolution into the past, empirical studies of various organisms have illuminated histories replete with changes in population size, migrations, population splits, and mergers. Demographic inference generally operates by fitting simplified models of population history to patterns of genetic variation assumed to have no effect on the fitness of the organism. An important use of these models is provide approximate dates for historical events. It is also important to understand what the implications of these models, and the complex histories they attempt to represent, are for the distribution of biologically interesting types of genetic variation. The work presented here first addresses the consequences of population history for deleterious genetic variation and genetic variation affecting quantitative traits. The investigations center around (1) how divergent histories between examples of African and Out-of-Africa populations have led to differences in the distribution of deleterious variation, and (2) how arbitrary models of demographic history affect the distribution of quantitative traits. Finally, (3) the dog/wolf mutation rate is estimated and used to scale demographic models of dog domestication.